From owner-metabolic-reg@net.bio.net Tue Sep 21 06:50:00 1999 Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!news.demon.co.uk!demon!fssc.demon.co.uk!not-for-mail From: "Herbert M Sauro" Newsgroups: bionet.metabolic-reg Subject: Re: Universal format for storing pathways and models Date: Tue, 21 Sep 1999 08:39:08 +0100 Message-ID: <937899606.7504.0.nnrp-08.c2de3927@news.demon.co.uk> References: <40EF164E4C27D31192760000F847DF32519954@ukz206.ggr.co.uk> <937692632.667327@sirius.shome.eu.org> <7s216b$ug5$1@nnrp01.ops.uunet.co.za> <937750899.40114@sirius.shome.eu.org> <937852968.19861.0.nnrp-07.c2de3927@news.demon.co.uk> <937860976.418122@sirius.shome.eu.org> NNTP-Posting-Host: fssc.demon.co.uk X-NNTP-Posting-Host: fssc.demon.co.uk:194.222.57.39 X-Trace: news.demon.co.uk 937899606 nnrp-08:7504 NO-IDENT fssc.demon.co.uk:194.222.57.39 X-Complaints-To: abuse@demon.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 Lines: 119 Alex Sel'kov wrote in message news:937860976.418122@sirius.shome.eu.org... > > Is there a public specification of EMP, I've never seen one even though I've > > looked. > > In 1994 EMP was published on CD and companion book contains fromat > descripsion. Parsers also availiable. > You should put the EMP spec on the net. Can you give a very small example, eg an example to specify the following model: Note: X0 and X1 are boundary metabolties. X0 -> S1; k1*X0; 2 S1 -> X1; k2*S1; k1 = 1.2; k2 = 4.5; S1 = 0; X0 = 1.0; X1 = 0.0; > But anyway we need to develop "commertial grade" formal specifications, > programmers API, user guide e.t.c. Long delay with so trivial steps also > trivial - funding. Only in this year we can seriously think about development, > (I mean not prototypes and pilots but normal development: with schedule, > internal standarts, documented production process, professional team e.t.c) > and most of urgent things will be completed by the end of this year. > Perhaps we should think about a net wide effort? > By the way, you know any simulation software wich can import metabolic > pathways, stoichiometric matrixes e.t.c. from KEGG or Boehringer? ;) > Not that I know of. What are Boehringer pathways (apart fom the wall charts)? > > > From my point of view, we always have three questions: > > > > > > 1. "Why?" > > > > Because Gepasi and Scamp wanted to talk to each other. There have been a > > number of occasions when I wanted to run Geapis models but couldn't and I'm > > sure Pedro (Mendes) sometimes had the same problem but the other way round. > > > > And why not to think about other possible applications? Visualisation software? > Database search engines? Another software packages? > We have thought of other software packages. One reason for opting for a binary standard was that it would be easy for anyone to write a parser to read and export pmb files. So we thought that DBSolve for example could import and export pmb files, it would probably only take a day or two to write such a utility. If the standard were structured ascii it would take much longer for someone to write an importer, possibly weeks or more (syntax checking etc). The pml standard we are developing will be able to export pmb files. Note that the pmb file is fully extensible and portable, it has been designed so that any changes made to the standard will not make old pmb files redundant. There is some metabolic visualisation software which I've written called Talis, see my web site for details. I'm not such interested in database (I work with them all day anyway commerically) work, I'm much more keen on metabolic dynamics and engineering and understanding how such complex systems work. Trawling through database data and doing sql queries is not that interesting to me. We're in the process of defining a human readable spec for defining and manipulating metabolic pathways, the so-called pml standard. What I think is more important from my point of view is enabling 'ordinary' biochemists and molecular biologists to write and model systems without having to learn an unfamiliar syntax such as XML etc. Instead I think one should opt for a simple basic like language which everyone will be familiar with. > > > 2. "What?" > > > > What what? > > > > What to do. Formal specifications which explains concepts. > Ok I see. > > > 3. "How?" > > See pmb document. > > > > > I see. This is implementation. > > I can say only one thing - this solution is perfectly fits if you need exchange with > a very few model by occassion. But when we speak about thousands of models > with many various tools working simuntaniously on the same data - you can't > base your work on formats like pbm. Definitely not. > But the spec can exchange large models too, there is no limit to the size of model one can specifiy. > In any case I can't say that pbm is "bad" or "good". Simply such format > unfotutantely can't solve our (by example) problems. What precisely is the aim of the work you do? Thanks Herbert > > Regards, > > as .